US20110151440A1 - Screening for Arthrogryposis Multiplex in Bovines - Google Patents

Abstract

Provided are methods, materials and kits for analyzing DNA samples from bovine to determine whether the animal is a recessive carrier of a genetic mutation that is associated with arthrogryposis multiplex (AM). DNA-containing samples are analyzed by genetic testing to determine whether or not a deletion mutation is present in one of the alleles that are responsible for the AM genetic mutation. In an aspect the deletion encompasses the entirety of the ISG15 ubiquitin-like modifier (ISG15) gene. In an aspect the deletion further encompasses one or both of the 5′ regulatory region of the hairy and enhancer split 4 (HES4) and of the agrin (AGRN) gene and of the first two exons of the AGRN gene.

Description

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
• This invention was at least in part made with government support under AG 2004-34480-14417 and 58-5438-2-313 awarded by the USDA. The government has certain rights in the invention.
REFERENCE TO A SEQUENCE LISTING
• A sequence listing containing SEQ ID NOs:1-19 is submitted herewith and is specifically incorporated by reference.
BACKGROUND OF THE INVENTION
• Arthrogryposis Multiplex (AM), commonly referred to as “Curly Calf Syndrome,” is a genetic defect that has recently been reported in Angus cattle. Based on pedigree examination of affected calves, this genetic defect is determined to have an autosomal recessive mode of inheritance. Due to this recessive inheritance pattern, only calves that are homozygous (i.e., receiving a chromosome with the mutation from both parents) for the mutation causing AM are affected with multiple abnormalities most often including arthrogryposis (contracted or extended limbs with stiffened joints), scoliosis and kyphosis (abnormal curvature of the spine), and muscular hypoplasia (reduced muscle development). Less commonly, the syndrome is associated with mild hydrocephalus caused by inflammation of the brain. Calves are born dead or fail to thrive and die shortly after birth. Classification of normal appearing individuals (e.g., those that are homozygous for the normal allele or heterozygous or carriers of the mutation) is virtually impossible in the absence of planned breeding studies or test matings. Accordingly, there is a need for a test that can reliably identify whether an animal is a heterozygous or a carrier of the mutation.
• The American Angus Association® cattle breeders group recently became aware of a small number of calves born dead with bent and twisted spines. Subsequent monitoring of the situation provided further incidents of such calves being born. Reproductive technologies, where certain parents having beneficial traits are used frequently, can result in the observation of unwanted defects introduced in a breeding program. Good tracking of lineage, however, can provide the ability to breed out certain undesirable genes. In this case, extensive breeding and pedigree studies have revealed that AM has an autosomal recessive mode of inheritance. For the AM to be expressed, a calf must have inherited the defective gene from both parents. A calf that expresses the phenotype is “homozygous” for the mutant AM gene, and the parents of such a calf are “heterozygous carriers” for the mutant AM gene (homozygous animals do not survive to reproduce). It is virtually impossible in the absence of planned breeding studies or test matings to classify whether a normal appearing individual is a heterozygous carrier of the mutant AM gene (AM carrier or “AMC”) or is homozygous for the normal allele (AM free or “AMF”). Genetic screening is beneficial in avoiding loss of genetic resources due to culling based only on pedigree.
• Because heterozygous individuals appear normal, carriers of the trait cannot be identified by eye, and instead exhaustive and time-consuming familial analysis is required in order to identify potential carrier individuals. There is a need in the art for screens that can identify heterozygous carriers of AM by genetic testing to facilitate a breeding program that eliminates the genetic defect from the population. Such a screen requires an understanding of the genetic basis of the defect, including identification of the causative mutation within the DNA sequence. Disclosed herein is a mutation associated with AM and provided are various genetic tests to determine whether apparently normal individuals carry a defective gene associated with AM. The methods, products and kits provided herein permit testing of individuals to determine whether an individual is a carrier. Individuals that are carriers can be removed from the breeding population, thereby facilitating removal of this genetic defect from the population.
• While dramatic culling of suspected carriers would reduce the frequency of the mutation responsible for AM, such culling is long, expensive and can result in unnecessary reduction of beneficial genetic traits, as many of the culled animals would not be carriers of the mutation. Accordingly, there is a need in the art for a diagnostic or genetic screening test to determine whether or not an animal is a carrier of the mutation responsible for AM. Provided herein are materials and methods for screening animals to determine whether an animal is a heterozygous carrier of the mutant allele responsible for AM.
SUMMARY OF THE INVENTION
• The invention features screens, methods, kits and associated probes, primers and DNA sequences for diagnosing in an animal, the genetic defect responsible for AM. In particular, provided are accurate DNA-based diagnostic tests used to assess an individual's genotypic status for AM. The methods of the present invention are used to diagnose whether a phenotypically “normal” animal is a recessive carrier of a mutated gene which is associated with AM. In an embodiment, the method is for detecting a genetic defect in bovine genome that affects one or more of the Hairy and enhancer of split 4 (HES4) gene, the ISG15 ubiquitin-like modifier (ISG15) gene, and the agrin (AGRN) gene, and more particularly, a genetic defect that comprises a deletion mutation that affects function or expression of one or more of those gene products. The methods described herein are useful in detecting a deletion mutation in the bovine genome that results in loss of AGRN gene function, loss of HES4 function and/or loss of ISG15 function. In an aspect, the deletion is a sequence that is SEQ ID NO:3, plus SEQ ID NO:10 either contiguously upstream (SEQ ID NO:5) or contiguously downstream (SEQ ID NO:4) to SEQ ID NO:3, wherein about 23,363 base pairs are deleted, as reflected by comparing SEQ ID NO:1 (wildtype gene) to SEQ ID NO:2 (mutant AM gene).
• In an aspect, provided are methods, materials and/or kits for detecting a change or mutation in the DNA sequence of specific genes responsible for AM in an animal. The methods of the invention rely on the finding that the mutation associated with AM is a deletion mutation. The deleted portion of the DNA corresponds to a “middle region” of the DNA sequence. The adjacent sequence portions upstream and downstream of this middle region correspond to an “upstream region” and “downstream region”, respectively. A normal AM genome (e.g., “non-mutant” or “wildtype”) has upstream, middle and downstream regions in a contiguous configuration (SEQ ID NO:1). A mutant AM genome has at least one allele comprising the corresponding upstream and downstream regions in a contiguous configuration (e.g., the middle region is absent; see, e.g., SEQ ID NO:2). In an embodiment of the present invention, each strand of a wildtype DNA molecule to be tested or screened comprises three regions: (i) an upstream region; (ii) a downstream region, and (iii) a sequence between the upstream and downstream regions. In a mutant DNA molecule associated with AM, the sequence between the upstream and downstream regions is deleted.
• Accordingly, diagnostic assays and DNA tests provided herein determine whether or not a deletion mutation is within the region of the genome that encodes for (or is at least partially responsible for expression of) one or more of HES4, ISG15 or AGRN. In an aspect, the deletion results in loss-of-function of AGRN. In an aspect, the deletion results in loss-of-function of ISG15. In an aspect, the deletion results in loss-of-function of HES4. In an embodiment, the bovine genome comprises the bovine DNA sequence of SEQ ID NO:1 (wildtype) and/or SEQ ID NO:2 (mutant AM—found in AM-expressing phenotype and heterozygous AM carriers), wherein the middle portion corresponds to a deletion from bases 6508 to 29,854 of SEQ ID NO:1 (cross-referenced as SEQ ID NO:3) plus an additional 16 base pair sequence of SEQ ID NO:10 that is contiguous to either the upstream end (see SEQ ID NO:5) or downstream end (see SEQ ID NO:4) of SEQ ID NO:3.
• An example of an upstream region DNA sequence is at least a portion of the sequence upstream of, and contiguous to, base 6,491 or 6,507 of SEQ ID NO:1, such as the upstream contiguous 100, 200, 3500, or between about 100 to 300 bases or any subrange thereof, of SEQ ID NO:1. In an embodiment, the upstream region corresponds tobases 1 to 6491 of SEQ ID NO:1 (e.g., SEQ ID NO:6) or to bases 1 to 6507 of SEQ ID NO:1 (e.g., SEQ ID NO:7). In an embodiment, the upstream region corresponds to bases 1872 to 6491 of SEQ ID NO:1 or to bases 1872 to 6507 of SEQ ID NO:1. In another embodiment, upstream corresponds tobases 1 to 429 of SEQ ID NO:2, or upstream and contiguous to base 429 or 445 of SEQ ID NO:2, such as an upstream region having a length of 100 basepairs, 200 base pairs, or between about 100 and 300 basepairs in length.
• An example of a downstream region DNA sequence is at least portion of the sequence downstream of, and contiguous to, base 29,854 or 29,870 of SEQ ID NO:1, such as the downstream contiguous 100, 200, 5,000, or between about 100 to 300 bases or any subrange thereof of SEQ ID NO:1. In an embodiment, the downstream region corresponds to bases 29855 to 35035 of SEQ ID NO:1 (e.g., SEQ ID NO:9) or to bases 29871 to 35035 of SEQ ID NO:1 (e.g., SEQ ID NO:8). In another embodiment, downstream corresponds to bases 429 to 751 or bases 445 to 751 of SEQ ID NO:2, or downstream and contiguous to base 429 or 445 of SEQ ID NO:2, such as a downstream region having a length of 100 basepairs, 200 base pairs, or between about 100 and 350 basepairs.
• The DNA analysis optionally comprises PCR to amplify specific DNA sequences, thereby providing for accurate and reliable diagnostic and screening methods of the present invention. Primers are selected that flank regions of interest, including potential breakpoints or portions of the DNA sequence corresponding to the middle region. In an embodiment, a forward primer is selected that is capable of specific binding to the upstream region and a reverse primer is selected that is capable of specific binding to the downstream region. Such a primer pair cannot amplify DNA if the middle region of about 23 kb of DNA is present (e.g., wildtype), because the primers are sufficiently separated that amplification cannot efficiently occur. In the presence of the specifically exemplified deletion mutation, however, the two primers are close enough, for example less than about 5,000 base pairs, or less than 1,000 base pairs, or less than about 500 base pairs, for efficient amplification. In an exemplified embodiment, the primers are 22 bases in length and separated by 463 (or 532) bases, providing an amplified DNA product that is 507 (or 576) bases or basepairs in length. The amplified DNA product is detected by any means known in the art, including with a probe (radioactive, fluorescent, luminescent or colored, for example), nuclease assay, by a DNA sequencer, or by running the sample on an electrophoretic gel and detecting the DNA of an expected size.
• Various forward and reverse primers (as well as probes) useful in the present invention are described herein and are shown in the SEQ ID NOs:1 and 2 provided in Tables 1 and 2, respectively, in bold and in bold and underline. The probes and primers of the present invention comprise those having sequences corresponding to, or a reverse complement of, the bold or the bold and underlined sequences outlined in the Tables 1-2, and any other probes or primers useful in classifying genotype for the AM mutation as a person of ordinary skill in the art can design and make based on hybridization requirements, binding specificity, and sequence homology. Reverse primers correspond to reverse complementary sequences of the DNA sequences in bold or in bold underline. The invention includes the reverse complement sequences to obtain primer and probe sequences that specifically bind to targets, including specific targets within or spanning each of one or more of the upstream, middle and downstream regions provided in SEQ ID NOs:1-10, or potential breakpoint regions. A reverse primer is paired with a forward primer having a sequence with a region identical to at least a portion of the DNA sequences of any of SEQ ID NOs:1-10, including a region identical to at least a portion of the upstream region DNA sequence. Each of the indicated primers are capable of specific binding in that they do not span a DNA repeating sequence and do not have significant homology with any other DNA sequence of similar length that could introduce uncertainty into the assay. For example, the probes or primers may have up to seven adjacent nucleotides in common and have approximately 70% homology, including 70% and greater, with the corresponding target sequence given by a portion of any of SEQ ID NOs:1-10, or reverse complement thereof. Accordingly, the probes and primers are not limited to those explicitly exemplified, but encompass other probes and primers that one of ordinary skill in the art identifies as capable of specific binding. In addition, probes and primers specific to the breakpoint regions, (shown by the triangles in Table 2 and corresponding to between bases 429 and 430 of SEQ ID NO:2 or between bases 445 and 446 of SEQ ID NO:2); upstream breakpoint between bases 6491 and 6492 or 6507 and 6508 of SEQ ID NO:1; downstream breakpoint between bases 29854 and 29855 or 29870 and 29871 of SEQ ID NO:1 are particularly useful in DNA-based analysis for determining AM deletion mutation status.
• A two primer system that distinguishes between a (deleted) mutant gene and a normal gene relies simply on the presence or absence of an amplified DNA product, for example. If the primer pair flanks the potential deletion region, an amplified DNA product only occurs for the mutant and the animal is classified as “normal” if there is no amplified DNA product. Similarly, if the primer pair spans the breakpoint region (e.g., one primer specifically binds only if upstream and middle (or middle and downstream)), absence of amplified product indicates the animal has a mutant allele. Accordingly, for quality control, addition of a third primer to the forward and reverse primer pair may be desirable so that two distinguishable DNA products are generated which can then be further distinguished based on a signal, such as by size or differentially-labeled probes. Preferably, the third primer is capable of specific binding to at least a portion of the middle region so that a DNA product corresponding to the third primer and the forward primer (or the third primer and the second primer, depending on the third primer location with respect to the location of the first and third primers), is amplified. In this manner, every sample processed will have at least one amplified DNA product, and in the case of AMC two, where the amplified product can be differentially detected and can serve as an internal control on PCR. Such a three-or-more primer system addresses a concern about whether lack of signal can be attributed to deficient PCR processing/procedures for an individual sample instead of whether or not there is a AM mutation. The third primer may be a reverse primer that is paired to the first primer, or alternatively may be a forward primer that is paired to the second reverse primer.
• In an aspect, primer pairs for PCR amplification are selected so as to obtain, under appropriate conditions of “no deletion mutation” or “deletion mutation”, amplification product. With current reagents and PCR processing conditions, such primer pairs may be separated by up to about 6-7 kb, although most techniques are within about 600 bp, 500 bp or 200 bp. Accordingly, the methods described herein do not require an exact relative separation distance between primer pairs, so long as primers used in tests relying on detecting a difference in DNA length of two or more amplification products provide amplification products of experimentally detectable different lengths. In an aspect, primer pairs are selected to be separated, under conditions where an amplification product is desired, by less than 6000 base pairs and more than 15 base pairs.
• In a particular embodiment, the DNA analysis further comprises providing one or more of a forward primer having the sequence of SEQ ID NO:11 (to specifically hybridize to the upstream region complementary strand corresponding to bases 6328 to 6349 of SEQ ID NO:1 or to bases 266 to 287 of SEQ ID NO:2), a reverse primer having the sequence of SEQ ID NO:13 (corresponding to the reverse complement of SEQ ID NO:12) (to specifically hybridize to the downstream region of bases 30,176 to 30,197 of SEQ ID NO:1 or to bases 751 to 772 of SEQ ID NO:2). Optionally, a third primer is directed to specific hybridization with a portion of the middle region and positioned to provide generation of an amplification DNA product with either of a corresponding forward primer (to the upstream region) or a corresponding reverse primer (to the downstream region). In an aspect, the third primer corresponds to a middle region target sequence corresponding to SEQ ID NO:14 (corresponding to bases 6882 to 6903 of SEQ ID NO:1; no corresponding sequence in SEQ ID NO:2, as that sequence has this middle portion deleted), and specifically a reverse complement thereof (e.g., SEQ ID NO:15). Accordingly, in the embodiment where the primers are SEQ ID NOs:11, 13 and 14, a normal allele will provide one amplified DNA product that is 576 bp in length and a mutant AM allele will provide one amplified DNA product that is 507 bp in length. An AMC will produce both size amplified DNA products.
• Various methods may be used to provide classification of the sample genotype as AMF or AMC. The amplified PCR product or the DNA from the sample can be analyzed directly by providing a DNA probe (or a primer for extension) that is capable of specific binding to a region that identifies the DNA as normal (e.g., a portion of the middle region is present, or one or both of the contiguous ends of the middle and upstream or middle and downstream regions are present) or is capable of binding to a region that identifies the DNA as a mutant (e.g., the breakpoint region). Alternatively, the DNA can be analyzed by DNA sequencing and comparing the sequences to those provided herein to determine whether there is a mutation. The amplified DNA products may be further analyzed to characterize the length of the products, such as by being run on a size-separating gel. Any of these techniques may be optionally combined together to generate an improved signal or additional information, as desired.
• Oligonucleotide probes or primers of the present invention can be used with any of the methods disclosed herein. Probe or primer sequences are designed based on the DNA sequences provided herein, and specifically hybridize or bind to DNA regions so as to provide information about whether or not a deletion mutation associated with AM is present, such as deletion affecting one or more of the HES4, ISG15 ubiquitin-like modifier and/or the AGRN gene. In an embodiment, the probes or primers comprise a purified oligonucleotide having a length of about 15 to about 50 nucleotides. Particular specific binding sites include those encompassing bases T429 and G430, 445A and 446C of SEQ ID NO:2 (e.g., break-points), by the middle region defined by SEQ ID NO:3 (or, alternatively one of SEQ ID NOs:4 or 5) and contiguously associated upstream and downstream flanking regions.
• The methods and materials provided herein can be used on any animal, and is preferably used in bovine to detect the presence or absence of a AM mutation, and is particularly useful in testing animals characterized as an Angus breed, for example Angus and their composites that are susceptible to AM. The tests and materials can be used with the DNA obtained from any animal tissue or fluid. Convenient samples are obtained from hair, blood or semen.
• Provided are isolated and purified nucleic acid molecules of any of the sequences disclosed herein (e.g., those of Tables 1-3, and any of the SEQ ID NOs), or including at least a functional fragment thereof. Useful primers and probes include those that specifically bind a target sequence that resides in at least a portion of a particular DNA region such as an upstream region, downstream region or a middle region. Other useful oligonucleotide primers or probes include those that specifically bind a breakpoint or those that specifically bind two adjacent regions, such as an isolated and purified nucleic acid molecule comprising at least a functional fragment of a deletion breakpoint that is the causative agent of AM. The probes or primers can be of any length and homology, so long as the length and homology is sufficient to result in specific binding to a specified target region, or any non-specific binding is confined to a region that does not adversely impact the assay. In an embodiment, the probe or primer is an oligonucleotide or a DNA sequence that ranges in size from about 15 to 80 bases, or about 18 to 60 bases, or about 20 to 25 bases. Desirably, at least 12, at least 15, or preferably at least 20 bases are homologous to the target sequence. In an embodiment, all the primer or probe base are homologous (e.g., complementary) to the target sequence. Exemplary probe or primer sequences are provided in Tables 1 and 2 in bold, and also in bold and underline.
• Kits comprising any of the oligonucleotide probes or primers disclosed herein are within the scope of the invention. The kits can further comprise instructions for appropriate DNA processing, hybridization and/or PCR conditions, and for visualizing or detecting amplified DNA products.
• For quality control, the kit optionally comprises DNA test samples that are a positive control (e.g., a mutant DNA sample comprising the breakpoint indicated in Table 2) and/or test samples that are a negative control comprising the middle region and associated flanking upstream and downstream regions, as summarized in Table 1 and SEQ ID NO:1. These controls can comprise DNA sequences corresponding to expected DNA-amplified products from the primers of the kit, or can be isolated and purified DNA sequences corresponding to wildtype or to normal and/or AM mutation that can be used by the probes or primers of the kit.
• Without wishing to be bound by any particular theory, there can be discussion herein of beliefs or understandings of underlying principles or mechanisms relating to the invention. It is recognized that regardless of the ultimate correctness of any explanation or hypothesis, an embodiment of the invention can nonetheless be operative and useful. For example, there is tolerance in the specific sequence and breakpoints, and such variation may be accommodated by one or more of the materials and methods provided herein such that an operative and useful invention remains.
BRIEF DESCRIPTION OF THE DRAWINGS
• FIG. 1: Photograph of a gel image demonstrating the diagnostic for identifying Arthrogryposis Multiplex (AM) in cattle. Each row represents the results from amplification of genomic DNA corresponding to 23 different animals (a total of 92 animals are shown). In the gel, the smaller amplified DNA (507 bp fragment identifies a deletion mutation) runs further than the larger amplified DNA (576 bp fragment identifies a normal allele). Thirty-one animals are tested as heterozygous for the mutation causing AM (AMC) as revealed by the presence of two bands: a 507 bp fragment and a 576 bp fragment that corresponds to the normal DNA sequence.
DETAILED DESCRIPTION OF THE INVENTION
• As used herein, “diagnosing” refers to classifying an animal whose DNA is being tested into a specific genotype status related to AM. For example, an animal that is homozygous for the normal variant are referred to as AM-Free (AMF), indicating the animal has been tested for the causative mutation and has been found to be “free” of the causative mutation responsible for AM. If the individual tested is found to be heterozygous or “carriers” for the mutation, meaning that the individual possesses one normal allele and one mutant allele, they are classified as AM-Carrier (AMC). An AMC individual can pass on the mutation, and due to the manner of passage of genetic information to off-spring, the frequency of passage to offspring is about 50%. Generally, an individual homozygous for the AM mutation is an animal expressing the AM phenotype, meaning that the affected calf can be diagnosed or classified simply by observing the calf's phenotype, meaning testing is unnecessary in order to identify the animal as AM-Affected (AMA). As discussed AM is a lethal mutation so that AMA individuals do not survive to breed, and so the test, in and of itself is not necessary to remove the affected individual from the breeding pool. In various embodiments, however, testing of the genetic materials from AMA animals is provided as a positive control, such as in methods and kits for diagnosing AM. In addition, testing of such individuals can be beneficial to confirm the underlying basis of the mutation and to confirm the mutation remains conserved with respect to the deletion mutation provided herein.
EXAMPLE 1Characterization of the Genetic Basis of the Mutation
• The accurate identification and subsequent selection against carriers of the AM mutation is the only method that can be used to eliminate this genetic defect from the population, without concurrent loss of genetic resources due to culling based only on pedigree. The development of a method to accurately and efficiently determine the genotype status of an individual is dependent on understanding the molecular basis of the defect (i.e., identification of the causative mutation within the DNA sequence). The mutation causing AM is identified as a deletion of about 23,363 base pairs. This deletion encompsses the 5′ regulatory region of the hairy and enhancer of split 4 (HES4) gene, the entirety of the ISG15 ubiquitin-like modifier (ISG15) gene, and the 5′ regulatory region and first two exons of the agrin (AGRN) gene. The role of HES4 and ISG15 in disease pathology is unclear, however based on the functional role of AGRN in development of the neuromuscular junction it is the most likely causative gene for the pathology. The mutation results in a complete loss-of-function of AGRN thus producing the disease phenotype when an animal is homozygous for the deletion-containing chromosome. Gene “knock-out” models of AGRN in mice result in similar pathologies (Harvey et al., 2007). Using the DNA sequence information that has been generated, various DNA-based diagnostic tests are provided to accurately determine an individual's genotype with respect to AM (particularly AMC or AMF). Thus, the genotype of an animal can be obtained by analysis of any DNA containing sample such as blood, semen or hair follicles.
• Table 1 summarizes relevant technical data corresponding to the identification of the causative mutation for AM. SEQ ID NO: 1 (also provided in Table 1) corresponds to the bovine DNA sequence that encompasses the region affected by the deletion mutation. Exons corresponding to the protein coding sequence of HES4 (red—labeled “R”), ISG15 (green—labeled “G”), and AGRN (yellow—labeled “Y”), are highlighted. The deletion mutation causing AM is highlighted in grey (corresponding to bases 6508 to 29854 of SEQ ID NO:1; cross-referenced as SEQ ID NO:3). Note thatexons 1 and 2 of the AGRN gene is contained within the deleted segment as well as the entirety of the ISG15 gene.
• Exemplary primer sequences used for sequencing, defining the deletion breakpoint, and diagnostic testing are in bold and bold/underline with forward primers in green and reverse primers in red. Various specific SEQ ID NOs and descriptions thereof are summarized in Table 3.
• Table 2 and SEQ ID NO: 2 is generated by PCR amplification across the deletion breakpoint boundaries in affected calves and heterozygotes. Triangles in the sequence of Table 2 indicate the position of the deletion breakpoint that corresponds to the joining at a simple 16 bp sequence motif (highlighted in orange). Alignment between SEQ ID NO:1 and SEQ ID NO:2 demonstrates that SEQ ID NO:2 represents flanking DNA sequences separated by 23,363 bp on the normal chromosome.
• AM is observed in Angus cattle and Angus influence cattle. In particular, any animal that can be traced back to a particular individual by breeding records as the probable source of the mutation (e.g., Rito 149 of J845 7T26 Registration 9238034) is potentially a carrier of the defective gene responsible for AM. Analysis of lineage lines indicates that AM is an autosomal recessive disease. Accordingly, many animals in the breeding population are potential “heterozygous carriers”, e.g., animals that have one copy of the gene responsible for AM (AMC). This number is estimated to be as high as 10%. The methods and compositions of matter presented and claimed herein are particularly useful for diagnosing whether or not an animal is a recessive carrier of the defective gene responsible for AM. Animals identified as AMC can be removed from the breeding population so as to breed out the gene responsible for AM, or alternatively, bred with AMF with the offspring then tested for the AM mutation. The tests and materials provided herein, however, are compatible with different breeds such as breeds wherein this mutation may arise in the future.
• As used herein, “DNA sample” includes the part of the bovine genome that is a locus for AM. In particular, it is that part of the genome associated with expression of one or more of AGRN, HES4 and ISG15 genes or gene products. Methods provided herein are, accordingly, useful for detecting whether or not there is a deletion mutation that when inherited from both parents results in phenotypic expression of AM. An animal that is a heterozygous carrier of this deletion mutation is said to have a mutation that is associated with AM or is an AMC.
• “Obtaining” is used broadly to refer to any method of obtaining a biological sample that contains DNA, and specifically a sample that contains at least a portion of the genome spanning a region associated with the mutation that is a causative agent of AM. The sample can be from any tissue, so long as the sample contains DNA that is not significantly degraded, and can be fresh, frozen or otherwise preserved. For example, blood, semen or hair are relatively easily obtained and can be processed for immediate analysis or stored for later transport, processing and analysis. Although DNA may be obtained from other types of tissue containing DNA such as skin or muscle, those types of tissue may not be preferred as they are more difficult to obtain, store, transport and process compared to blood or semen.
• As used herein, “analyzing” broadly refers to any technique that reveals genetic information, particularly whether or not a DNA sample contains an allele comprising a mutation associated with AM. In a preferred embodiment, the technique comprises PCR processing to amplify selected DNA sequences to yield information about the status of the sample. Other techniques, including DNA hybridization with probes, DNA sequencing, DNA separation by gel electrophoresis and others known in the art can be optionally combined with PCR to generate improved signals.
• The portion of the bovine genome that is involved with AM, including those portions useful for determining whether an animal is normal or a heterozygous carrier of AM, can be divided into three regions: (i) an upstream region; (ii) a downstream region; and (iii) a middle region, wherein the middle region forms a contiguous configuration with the upstream region at one end and the downstream region at the other end. “Contiguous configuration” refers to two or more DNA sequences forming a continuous DNA strand, wherein there are no additional DNA sequences between adjacent strands. Processes and materials provided herein for identifying carriers of AM is based on the discovery that the AM mutation is associated with deletion of the middle region, such that the upstream region and downstream region form a contiguous configuration. DNA analysis of known AM mutant genes reveals that the mutant gene has a deletion, whose size and location tends to be conserved among different animals. With this information; methods and related compositions of matter are presented herein that are useful in determining whether or not an animal is a recessive carrier of a AM mutant gene by determining the presence or absence of this middle region, either directly (such as by probing) or indirectly (such as measuring length of an amplified product, with one unique length indicating no mutation and another unique length that is different indicating mutation).
• Polymerase Chain Reaction (“PCR”) is a technique in which cycles of denaturation, annealing with primer, and extension with DNA polymerase are repeatedly used to amplify the number of copies of a DNA segment, up to and greater than 10⁶times. PCR and associated PCR conditions are known in the art and are described more fully in U.S. Pat. Nos. 4,683,195 and 4,683,292, which are herein incorporated by reference. A “primer” is a single stranded oligonucleotide or DNA fragment which hybridizes to a DNA strand. In PCR, primers are generally paired, with a 5′ forward primer that hybridizes with the 5′ end of the DNA sequence to be amplified, and a 3′ reverse primer which hybridizes with the complement of the 3′ end of the sequence to be amplified. The amplified DNA sequence encompasses the target sequence hybridized by both primers, as well as the intervening sequence between both primer target sequences. Any portion of the DNA sequences provided herein can be used as a probe or primer, so long as the probe or primer sequence specifically binds one target. Such specific binding improves the reliability of DNA-based screens useful for identifying carriers of the AM mutation.
• The oligonucleotide primers and probes are generally selected for their ability to specifically bind to at least a portion of the upstream, downstream or middle DNA region. “At least a portion” refers to the embodiment where the target DNA sequence spans adjacent regions, including upstream-downstream (e.g., AM mutant), upstream-middle (e.g., no AM mutant) or middle-downstream regions (e.g., no AM mutant). In an aspect, the oligonucleotide is isolated and purified DNA.
• As used herein, “Angus” refers to any bovine animal with any Angus ancestry.
• Analyzing DNA encompasses any means known in the art: cleavage, where cleavage is dependent on whether or not there is a deletion mutation; hybridizing of probes, where probe binding is dependent on whether or not there is a deletion mutation; PCR amplification, where the presence of amplification products, or the size of the amplification products where the size depends on whether the deletion mutation is present; DNA sequencing; etc. The invention can be practiced with any DNA detection methods known in the art, including any future-arising detection methods. Analysis methods rely on the discovery of a deletion mutation that is associated with AM, as reflected in the difference between the wildtype genetic sequence (SEQ ID NO:1) and the AM mutant genetic sequence (SEQ ID NO:2), and more specifically, the recognition that a large deletion mutation that is located within a defined location in the genome is associated with the disease (SEQ ID NO:3, corresponding to breakpoint between bases 6491 and 29855 or 6507 and 29871 of SEQ ID NO:1). Some examples of methodology that can be useful in detecting whether or not a large deletion is present include U.S. Pat. No. 4,683,202 (Process for Amplifying Nucleic Acid Sequences), U.S. Pat. Nos. 6,013,444, 6,225,093 US Pat. Pub Nos. 2006/0063191 (Detecting Nucleic Acid Deletion Sequences) and 2009/0239212.
• The typical DNA deletion of the AM gene is greater than about 23 kb (e.g., the difference between the central portions of SEQ ID NO:1 and SEQ ID NO:2 is a 23363 length deletion in SEQ ID NO:2 corresponding to the sequence of SEQ ID NO:3 plus the sequence of SEQ ID NO:10 that is either contiguously upstream or downstream of SEQ ID NO:3, such as SEQ ID NO:4 or SEQ ID NO:5). Accordingly, if one of SEQ ID NOs:4 or 5 is present (e.g., the genome is from wildtype), under typical PCR conditions (e.g., “short PCR conditions”), a primer pair located on either side of this deletion sequence will not generate any amplified product (the primers are spaced too far apart). If, however, the mutation is present and one of SEQ ID NO:4 or SEQ ID NO:5 is deleted from SEQ ID NO:1, the primer pair is then sufficiently close to result in generation of an amplified DNA product that is then detected. Accordingly, a person of ordinary skill in the art will recognize that any number of probes/primes may be designed and constructed for use with the DNA tests described herein, so long as the probes or primers exhibit specific binding to the target of interest.
• In the use of the oligonucleotides or polynucleotides as probes, the particular probe is labeled with any suitable label known to those skilled in the art, including radioactive and non-radioactive labels. Typical radioactive labels include³²P,³⁵S, or the like. Non-radioactive labels include, for example, ligands such as biotin or thyroxine, as well as enzymes such as hydrolases or peroxidases, or a chemiluminescer such as luciferin, or fluorescent compounds like fluorescein and its derivatives. Alternatively, the probes can be made inherently fluorescent as described in International Application No. WO 93/16094.
• Various degrees of stringency of hybridization can be employed. The present invention contemplates nucleic acid sequences which hybridize under low, moderate or high stringency hybridization conditions to the exemplified nucleic acid sequences set forth herein. Duplex formation and stability depend on substantial complementarity between the two strands of a hybrid, and a certain degree of mismatch can be tolerated. The more stringent the hybridization conditipns, the greater the complementarity that is required for duplex formation. Stringency can be controlled by temperature, probe concentration, probe length, ionic strength, time, and the like. Preferably, hybridization is conducted under moderate to high stringency conditions by techniques well known in the art, as described, for example in Keller, G. H., M. M. Manak (1987)DNA Probes,Stockton Press, New York, N.Y., pp. 169-170, hereby incorporated by reference. For example, stringent conditions are those that (1) employ low ionic strength and high temperature for washing, for example, 0.015 M NaCl/0.0015 M sodium citrate (SSC); 0.1% sodium lauryl sulfate (SDS) at 50° C., or (2) employ a denaturing agent such as formamide during hybridization, e.g., 50% formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mM NaCl, 75 mM sodium citrate at 42° C. Another example is use of 50% formamide, 5×SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5 times Denhardt's solution, sonicated salmon sperm DNA (50 μg/ml), 0.1% sodium dodecylsulfate (SDS), and 10% dextran sulfate at 4° C., with washes at 42° C. in 0.2×SSC and 0.1% SDS.
• An example of high stringency conditions is hybridizing at 68° C. in 5×SSC/5× Denhardt's solution/0.1% SDS, and washing in 0.2×SSC/0.1% SDS at room temperature. An example of conditions of moderate stringency is hybridizing at 68° C. in 5×SSC/5× Denhardt's solution/0.1% SDS and washing at 42° C. in 3×SSC. The parameters of temperature and salt concentration can be varied to achieve the desired level of sequence identity between probe and target nucleic acid. See, e.g., Sambrook et al. (1989) supra or Ausubel et al. (1995)Current Protocols in Molecular Biology,John Wiley & Sons, NY, NY, for further guidance on hybridization conditions.
• In general, salt and/or temperature can be altered to change stringency. With a labeled DNA fragment >70 or so bases in length, the following conditions can be used: Low, 1 or 2×SSPE, room temperature; Low, 1 or 2×SSPE, 42° C.; Moderate, 0.2× or 1×SSPE, 65° C.; and High, 0.1×SSPE, 65° C.
• “Complement” or “complementary sequence” means a sequence of nucleotides which forms a hydrogen-bonded duplex with another sequence of nucleotides according to Watson-Crick base-pairing rules. For example, the complementary base sequence for 5′-AAGGCT-3′ is 3′-TTCCGA-5′. This invention encompasses complementary sequences to any of the nucleotide sequences described or claimed herein.
• A “functional fragment” of a nucleic acid is a partial sequence of the nucleic acid molecule such that the functional fragment has utility as a probe, primer or a target sequence for specific binding to a complementary probe or primer in the present invention, for example. A functional fragment that is a probe or a primer is useful for diagnosis, sequencing or cloning of the portion of the DNA genome that is associated with AM, including the portion of the genome that encodes or regulates expression of one or more of HES4, ISG15 or AGRN genes or gene products thereof, and that portion of the genome that comprises a deletion mutation associated with AM.
• In accordance with the processes provided herein, there is provided a purified and isolated nucleic acid molecule which regulates and encodes for AGRN protein. Desirably, the nucleic acid molecule is a DNA isolated from Angus, Angus composites or other bovine suspected of having the AM mutation. Further encompassed are nucleotide sequences for probes and primers to various portions of the genome associated with the AGRN gene, and in particular probes and primers that bind specifically to an upstream region, downstream region, or a middle region, wherein the middle region corresponds to a mutation deletion associated with AM. Given a particular sequence, the generation of primers to that sequence is well known in the art. Sequencing and diagnostic primers are typically 20 to 28 base pairs, more preferably 22 base pairs in length, and generally match the sequence of interest between approximately 90% to 100%, most preferably approximately 100%. Primers are typically approximately 20 to 34 base pairs in length, more preferably 21 to 24 base pairs in length, with annealing temperatures in the 50 to 70° C. range. Gene probes are preferably approximately 1 kb in length comprising the gene of interest to be probed.
• Particular probe or primer sequences are selected for their ability to bind a single specific region of the DNA sequence in one or more of (or regions thereof) SEQ ID NOs:1-10, 16-19 (e.g., “specific binding”), but not to other genomic loci. As used herein, “specific binding” or “binds specifically” refers to an oligonucleotide (e.g., a primer or probe) that is sufficiently selective in hybridizing the target sequence so as to result in DNA analysis that is reliable and accurate in identifying DNA having an AM mutant allele. A probe or primer that is capable of specific binding to a DNA target sequence does not hybridize in significant amounts (e.g., measurable) amounts to a non-target sequence. To ensure specific binding, a number of different considerations are employed. For example, none of the target sequences should be located in DNA repetitive elements. In addition, potential target sequences can be analyzed against the remainder of the sequence to determine whether there are other regions with significant homology. “Homology” or “sequence identity” means the proportion of base matches between two nucleic acid sequences. When sequence homology is expressed as a percentage, e.g., 50%, the percentage denotes the fraction of matches over the length of sequence that is compared to some other sequence. Gaps (in either of the two sequences) are permitted to maximize matching. When using oligonucleotides as probes, the sequence homology between the target nucleic acid and the oligonucleotide sequence is generally not less than 17 target base matches out of 20 possible oligonucleotide base pair matches (85%); preferably not less than 9 matches out of 10 possible base pair matches (90%), and more preferably not less than 19 matches out of 20 possible base pair matches (95%). A primer or probe sequence of the present invention is considered capable of specific binding if there is less than 80% homology, less than 70%, and preferably less than 50% homology (corresponding, to a 20 base pair probe or primer having less than 16, less than 14, or less than 10 identically aligned bases) to other “non-target” sequences.
• Hybridizing the probes or primers with the DNA sample under stringent conditions also reduces the likelihood of binding to regions other than the target region. In general, probes or primers having higher homology to other sequences besides the target sequence can be hybridized under more stringent conditions than probes or primers having lower homology.
• For regular PCR conditions, the location of primer pairs are preferably separated by less than about 6,000 base pairs, less than about 2,000 base pairs, less than about 500 base pairs, or separated by a range that is less than or equal to about 700 base pairs and greater than or equal to about 400 base pairs, thereby ensuring efficient amplification. Processes provided herein are not, however, limited to a specific primer separation distance; the constraint is the ability of the primers to generate amplified DNA. In an aspect, the method for identifying AM carriers relates to a PCR method and primers that, when expressed, provide an indication of whether the sample is from an animal that is a carrier of AM. In an aspect, the identification is by determining a length of the expressed fragment, with one length indicating a normal sequence and another length indicating a mutated sequence. In an aspect, the primers are selected so that the normal chromosome amplification fragment is longer than the fragment amplified from a mutant chromosome corresponding to the deletion mutation. In an aspect, the lengths are reversed.
• As used herein, the terms “isolated and/or purified” refer to in vitro isolation of a DNA molecule from its natural cellular environment and from association with other components of the cell, such as nucleic acid, so that it can be sequenced, replicated, amplified and/or expressed. An “isolated and purified nucleic acid molecule” is a nucleic acid the structure of which is not identical to that of any naturally occurring nucleic acid. This term covers, for example, DNA which has part of the sequence of a naturally occurring genomic DNA, but does not have the flanking portions of DNA found in the naturally occurring genome. The term also includes, for example, a nucleic acid incorporated in a vector or into the genome of a cell such that the resulting molecule is not identical to any naturally occurring vector or genomic DNA.
EXAMPLE 2DNA-Based Tests to Detect AM
• Those of ordinary skill in the art will recognize that any number of DNA-based diagnostic tests can be developed that detect the presence or absence of a deletion on the order of greater than about 15,000 base pairs, or greater than about 20,000 base pairs, or about 23,363 base pairs (see, e.g., U.S. Pat. Pub. No. 20090239212). Given the length of the DNA sequence of SEQ ID NOs:1 and 2, the invention tolerates variation in both the precise breakpoint location and breakpoint sequence. For example, primers and probes can be designed so that the breakpoints (e.g., between bases 429-430 and bases 445-446 of SEQ ID NO:2) can vary, for example by plus or minus 20 base pairs, or plus or minus 10 base pairs, or plus or minus 5 base pairs or less, without affecting the ability of the probe or primer to specifically bind the target sequence and generate an output signal that can be used to determine the presence or absence of a deletion. One example of such designing is to ensure the probe/primer sequence is of adequate length, and also to target sequences that are greater than 5, greater than 10 or greater than 20 base pairs away from the potential breakpoint location.
• Any DNA test that detects, directly or indirectly, the breakpoint of the sequence that is associated with AM (e.g., between about bases 6,507 to 29,870 of SEQ ID NO:1 with the 16 base pair sequence of SEQ ID NO:10 contiguously either upstream or downstream of that deletion) of SEQ ID. NO:1 (wildtype) and corresponding mutant carrier (SEQ ID NO:2) may be used with the claimed methods, processes and kits. In particular, various methods may be used to detect corresponding breakpoint between about base T429 and G430 or A445 and C446 of SEQ ID NO:2 (as indicated by the triangles at these positions in the SEQ ID NO:2 shown in TABLE 2), whether directly (e.g., presence or absence of a signal or an amplification product) or indirectly (e.g., comparing a detected signal to a reference or another detected signal to classify the signal as arising from a mutation or a normal sequence) can be used as the basis of an assay for testing whether a subject is a carrier of the AM mutation. Such tests include but are not limited to DNA sequencing, hybridization and allele-specific extension. Any one or more tests may be used as desired, including primer extension, 5′ to 3′ exonuclease assays, or PCR, so long as a signal is generated that can be detected or measured either quantitatively or qualitatively.
• For example, PCR can be used to amplify appropriate DNA portions, and the amplified DNA run on a gel that separates DNA by size or other means for identifying DNA length. In this example, such a PCR test uses three different primer sequences, a first (forward) primer (primer 1) that binds upstream of the breakpoint, a second (reverse) primer (primer 2) that binds downstream of the breakpoint, and a third (reverse) primer (primer 3) that specifically binds to the middle region, corresponding to the deleted portion of DNA associated with the mutation responsible for AM. In this manner, as summarized in TABLE 4, primer pair 1-2 will generate an amplification product “I” if the deletion mutation is present. Similarly, primer pair 1-3 will generate amplification product “II” only if the middle region is present (e.g., no deletion mutation). Accordingly, if all three primers are used there will either be one amplified product (for AMF or AMA, but the AMF and AMA samples produce different length products) or two amplified products (for AMC—one allele “normal” the other allele having the deletion mutation for AM). Alternatively, if only primer pair 1-2 is used, a generated amplified product that is detected will indicate an animal that is at least AMC.
• The actual location of the target sequence to which the primer specifically binds is not critical, although under “normal” PCR conditions (e.g., not long range PCR conditions, see U.S. Pat. No. 6,225,093) it is preferable if the target sequence is within about 5 kb, or within 1 kb, or within about 400 to 600 bases of a potential breakpoint site and the other end of the to-be-amplified DNA sequence. Although the exact position of the primer is not critical, in one embodiment where the test is based on differences in amplified DNA length indicating the condition (e.g. AM carrier animal versus a normal animal), it is important that the difference in DNA amplification lengths be detectable or observable. In an aspect, the difference in DNA length between an AM carrier and a normal is 10% or greater (e.g., 576 bp in normal animal and 507 bp in an AM mutant). Of course, the required difference in length to be detectable or observable depends on the assay used to characterize length. For example, to reliably detect difference in lengths by running the DNA on a gel, an about 10% or greater length is desired. Alternatively, if the amplified products are sequenced, no difference in length is required.
• In one embodiment, the primers used with respect to a test that provides genotyping based on length of amplified product are as follows:
• First (forward) primer binding upstream region (SEQ ID NO:11): corresponding to bases 6328 to 6349 of SEQ ID NO:1.
• Second (reverse) primer binding downstream region (SEQ ID NO:13): reverse complement of SEQ ID NO: 12; corresponding to bases 30176 to 30197 of SEQ ID NO:1.
• Third (reverse) primer binding to middle region (SEQ ID NO:15): reverse complement of SEQ ID NO:14 (corresponding to bases 30176 to 30,197 of SEQ ID NO:1.
• As discussed, this combination of primers is used under standard PCR conditions to generate successful test results.
• DNA tests provided herein may be broadly characterized as “direct tests” or “indirect tests”. In a direct test, the detection or absence of a signal by itself is sufficient to identify the sample as at least AMC or as AMF. One example of a direct test is a method using only the two primers of SEQ ID NO:11 (bind upstream region) and SEQ ID NO:13 (bind downstream region) in that if a signal is generated, that is an indication of a mutant allele (see Table 4). If no signal is generated, the sample is AMF. In contrast, if all three primers are used, it is necessary to examine another parameter associated with the amplified products to assess the genotype (e.g., amplified product length), and such a test would be considered “indirect”. Other examples of direct tests include a probe that only binds if the deletion mutation is present, or primer extension where the primer only hybridizes to bovine DNA having the middle region deleted.
EXAMPLE 3Assay Characterization
• The first and second primers provided above (e.g., SEQ ID NOs:11,13) are each located on a separate side of the breakpoint. Accordingly, in a normal allele there is no amplification product attributed to the first (SEQ ID NO:11) and second (SEQ ID NO:13) primers as the intervening about 23 kb sequence between the first and second primers prevent generation of PCR-amplified DNA product. If there is, however, an allele for the AM disease (e.g., the intervening about 23 kb sequence is deleted), a first DNA product is amplified, wherein the DNA corresponds to the region encompassed by the first and second primers. The resultant length of this first DNA product is L₁₂. Alternatively, the first (SEQ ID NO:11) and third (SEQ ID NO:15) primers may be used to generate a DNA amplified fragment having length L₁₃and indicating a normal allele. The third primer resides in the deleted portion, and so a DNA product is not amplified for those alleles carrying the AM mutation. DNA of length L₁₃is generated only if the DNA sequence does not have the AM mutation. By selecting precise target sequences, the size of the amplification products generated byprimers 1 and 3 (L₁₃) can be different than the size generated byprimers 1 and 2 (L₁₂). The amplified DNA can be run on a gel to separate DNA by size, with the observed pattern dependent on whether or not the DNA from the subject to be tested is a carrier of an AM gene, as summarized in Table 4.
• FIG. 1 shows that two bands in a lane indicates a chromosome having one allele that has the mutation and another allele that is normal (e.g., see the top row, lanes: 1, 11, 13, 16, 18 and 21), thereby identifying the subject as a heterozygous carrier (AMC) of the AM gene. If only one band is observed, the subject is either normal (AMF) or the sample is from an individual that expresses the AM phenotype (AMA) (e.g., both alleles have the AM mutation). In this example, the single amplification product indicated by those lanes having only one band indicate AMF based on the 576 by size compared to the smaller 507 bp size for deletion mutation allele.
• FIG. 1 demonstrates one embodiment of a working diagnostic assay for both chromosomes. The exemplified primer sequences used for simultaneous amplification of fragments corresponding to either the normal (Table 1) or mutated (Table 2) sequence are highlighted in blue (indicated by “B”) in Table 1 (all three primers) and Table 2 (two primers—the third primer that would bind the middle region does not bind the mutant allele). The DNA fragment amplified from the normal chromosome is 576 bp in length and the fragment amplified from the deleted DNA sequence is 507 bp in length.
• The diagnostic assay is supported by two independent validation experiments including blind analysis of 91 samples of known genotype status based on progeny testing and analysis of phenotypically normal individuals of suspect pedigree. Results of the blind sample analysis are 100% concordant with the known genotypic status of the individuals. Among all phenotypically normal individuals of suspect pedigree no individual was genotyped as homozygous for the deletion mutation, indicating the association of the disease phenotype with only homozygous individuals (Chi-square=26.23, p<0.0001). Twenty-eight of 28 affected calves are genotyped as homozygous for the deletion. Frequency of the mutated allele is estimated at 10.52% by genotyping of 1,896 individuals.
• As summarized in Table 4, the third primer is not technically required in order to distinguish a normal animal from a heterozygous AM carrier. For quality control reasons, however, the third primer is optionally present and ensures that the DNA has been appropriately amplified and detected. As known in the art, the DNA need not be run on a gel, rather probes specific to each of the amplification products can be used, including radiolabeled, fluorescently labeled or any other detection substances and associated means for detecting the substance. Size separation and DNA labeling with, for example ethidium bromide is, however, a low-cost and easily performed assay for detecting AM heterozygous carriers.
• In an aspect, the amplified DNA products are detected, thereby identifying heterozygous carriers of a gene that is associated with AM. In an embodiment the DNA product is detected by running the DNA on a size-separation gel, wherein the expected sizes of each DNA product is known. Isolated and purified DNA sequences of the present invention corresponding to (1) normal, and (2) mutant can be used to ensure PCR conditions and DNA analysis is functioning appropriately.
• A unique, DNA-based diagnostic test that accurately determines the (AM) genotype status within cattle populations, including the Angus breed, through analysis of DNA containing samples i.e. blood, semen or hair follicles is important for eliminating this genetic defect from the population. Such a test eliminates the need for parental validation.FIG. 1 is an example of one such test where PCR amplification of the DNA from each individual is used to determine AM status.
• As understood in the art, genomic DNA comprises a sense strand and an antisense strand that is complementary to the sense strand. Unless expressly indicated otherwise, the sequences listed herein, are to the sense strand, running 5′ to 3′. Accordingly, the invention comprises the corresponding antisense sequences that are complementary to the listed sequences, and further include the reverse complementary sequences of all the primers and probes disclosed herein.
• All references cited throughout this application, for example patent documents including issued or granted patents or equivalents; patent application publications; and non-patent literature documents or other source material are hereby incorporated by reference in their entireties, as though individually incorporated by reference, to the extent each reference is not inconsistent with the disclosure in this application (for example, a reference that is partially inconsistent is incorporated by reference except for the partially inconsistent portion of the reference).
• Every formulation or combination of components described or exemplified herein can be used to practice the invention, unless otherwise stated.
• Whenever a range is given in the specification, for example, a temperature range, a size or separation base-pair range, a time range, or a composition or concentration range, all intermediate ranges and subranges, as well as all individual values included in the ranges given are intended to be included in the disclosure. It will be understood that any subranges or individual values in a range or subrange that are included in the description herein can be excluded from the claims herein.
• All patents and publications mentioned in the specification are indicative of the levels of skill of those skilled in the art to which the invention pertains. References cited herein are incorporated by reference in their entirety to indicate the state of the art as of their publication or filing date and it is intended that this information can be employed herein, if needed, to exclude specific embodiments that are in the prior art. All tables attached hereto (e.g., Tables 1-4) are part of the specification.
• As used herein, “comprising” is synonymous with “including,” “containing,” or “characterized by,” and is inclusive or open-ended and does not exclude additional, unrecited elements or method steps. As used herein, “consisting of” excludes any element, step, or ingredient not specified in the claim element. As used herein, “consisting essentially of” does not exclude materials or steps that do not materially affect the basic and novel characteristics of the claim. In each instance herein any of the terms “comprising”, “consisting essentially of” and “consisting of” may be replaced with either of the other two terms. The invention illustratively described herein may be practiced in the absence of any element or elements, limitation or limitations which is not specifically disclosed herein.
• One of ordinary skill in the art will appreciate that starting materials, materials, reagents, synthetic methods, purification methods, analytical methods, assay methods, and methods other than those specifically exemplified can be employed in the practice of the invention without resort to undue experimentation. All art-known functional equivalents, of any such materials and methods are intended to be included in this invention. The terms and expressions which have been employed are used as terms of description and not of limitation, and there is no intention that in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention claimed. Thus, it should be understood that although the present invention has been specifically disclosed by preferred embodiments and optional features, modification and variation of the concepts herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention as defined by the appended claims.
REFERENCES
• U.S. Pat. Nos. 6,759,192, 5,498,521, 6,013,444, 4,683,202, 6,225,093, 6,306,591; U.S. Pub. Nos. 2006/0063191; 20030203372; 20090239212; WO0246465, GB012566; GB0103156; GB0030076; AU0220920.

• TABLE 1
  SEQID NO: 1

• TABLE 2
  SEQ ID NO: 2, DELETION BREAKPOINT REGION:

  AAGCAGCAGCCAAGAAAGTAGAACTCACAAAAAATGAAGGATAATTGTT

  ACATTTCTGTTTGTTATTTCAAAGAAGCACGTGGAGGAAAGAGGGCTAA

  GCTTATTTTCGTGTTTGATGTTGTTTTCACTTTGAATTCCCTTGTGGGG

  CACAATCATGTTTTGAGTTTTGGGGATGCCAGCCCATGGGGCCTGGGCA

  GTCTTGTCTGCATCCCACAAACCTCTCTGGAGGCTCACTGTAGGCCTGA

  CGTTCTTGGGGCTGGGGAGGCCTCTCCTGAACTCTGAACTGATGTGGGA

  GGAAAAGGCAAATGAGCAAAATAAATAATGACATGGTTTCCAGAGACAG

  AAAGAAATGTGTAGGTTTTGGGGGGAGCCGAAAGCCTTCTTTCCACTGA

  GTGGTCTGGATGGTATTTTTGCAGTGAGCTCTGCT▴GGAGAAGGCAATG

  GCA▴CCCCACTCCAGTACTCTTGCCTGGAAAATCCCATGGACGGAGGAG

  CCTGGTGGGCTACAGTCCATGGGGTCGCTAAGAGTCGGACACGACTGAG

  CGACTTCACTTTCACTTTTCACTTTCATGCATTGGAGAAGGAAATGGCA

  ACCCACTCCAGTGTTCTTGCCTGCAGAATCCCAGGGACGGGGGAGCCTG

  GTGGGCTGCCGTCTCTGGGGTCGCACAGAGTTGGACACGACTGAAGCGA

  CTTAGCAGCAGTAGCAGCAGCAGCAGGTGCTATTTTTCTTAACCATTTT

  CTGGCCTCAGTTAGGATCCTGTGTCTTTCCTCAGTGCTGAAAAGGGAGA

  CTAGTAGTTGGATTATGTCATCCTA

  ▴Arrows indicate the position of the deletion breakpoint that corresponds to the joining at a simple 16 bp sequence motif (highlighted and underlined)

• TABLE 3
  SEQUENCE LISTING SUMMARY

  SEQ
  ID
  NO	DESCRIPTION	LOCATION IN SEQ ID NO: 1

  1	Normal: Upstream, Middle, Downstream Regions	1-35035
  2	Mutation: Upstream and Downstream (middle deleted)	1-6491 + SEQ ID NO:
  		10 + 29871-35035
  3	Middle Region - (deleted for AM mutant)	6508-29854
  4	Middle Region + SEQ ID NO: 10	6508-29870
  5	SEQ ID NO: 10 + Middle Region	6492-29854
  6	Upstream Region - (no SEQ ID NO: 10)	1-6491
  7	Upstream Region - (with SEQ ID NO: 10)	1-6507
  8	(No SEQ ID NO: 10) - Downstream Region	29871-35035
  9	SEQ ID NO: 10 + Downstream Region	29855-35035
  10	GGAGAAGGCAATGGCA	16 bp sequence at start or end of
  		deletion of SEQ ID NO: 3
  		6492-6507 or 29855-29870
  11	Primer 1 - upstream region	6328-6349
  12	Primer 2 - downstream region target sequence	30176-30197
  13	Primer 2 - downstream (reverse complement of SEQ ID	30176-30,197
  	NO: 12)
  14	Primer 3 - middle region [reverse primer]	6882-6903
  15	Primer 3 - middle region (reverse complement of SEQ ID	6903-6882
  	NO: 14)
  16	Truncated upstream (no SEQ ID NO: 10)	1872-6491
  17	Truncated upstream (with SEQ ID NO: 10)	1872-6507
  18	Upstream	6063-6491
  19	Downstream	29871-30234

• TABLE 4
  Summary of PCR product generated by
  three primers to determine AH status

  Primer Pair	AMF	AMC	AMA
  Primers 1-2	No product	Product I produced: L12	Product I
  (L12)		(from mutant allele)	produced: L12
  Primers 1-3	Product II	Product II produced: L13	No product
  (L13)	produced L13	(from normal allele)
  Primer 1: primer binds upstream region
  Primer 2: primer binds downstream region
  Primer 3: primer binds middle (e.g. mutant) region
  Primer 1-2: Length = L12
  Primer 1-3: Length = L13, where L12≠ L13for assays based on length difference

Claims (28)

1. A method of diagnosing a mutation in a bovine genome, wherein said mutation is associated with Arthrogryposis Multiplex (AM), said method comprising:

obtaining a DNA sample from the bovine; and

analyzing said DNA sample to determine the presence or absence of a deletion mutation for one or more of an AGRN gene, ISG15 gene or HES4 gene,

said DNA having an upstream region, a downstream region, and a middle region that separates said upstream region from said downstream region indicates absence of the deletion mutation; and

said DNA having said upstream region and said downstream region in a contiguous configuration is identified as having the deletion mutation.

2. The method ofclaim 1, wherein said deletion mutation results in loss of function of one or more of the AGRN, ISG15 or HES4 gene products.

3. The method ofclaim 1, wherein said middle region comprises the sequence of SEQ ID NO:3.

4. The method ofclaim 3, wherein said middle region is SEQ ID NO:4 or SEQ ID NO:5.

5. The method ofclaim 1, wherein said upstream region comprises the sequence from base 1 to 6491 of SEQ ID NO:1 (cross-referenced as SEQ ID NO:6), from base 1 to 6507 of SEQ ID NO:1 (cross-referenced as SEQ ID NO:7), from base 1872 to base 6491 of SEQ ID NO:1 (cross-referenced as SEQ ID NO:16), or from base 1872 to base 6507 of SEQ ID NO:1 (cross-referenced as SEQ ID NO:17).

6. The method ofclaim 1, wherein said downstream region comprises the sequence from base 29871 to 35035 of SEQ ID NO:1 (cross-referenced as SEQ ID NO:8), from base 29855 to 35035 of SEQ ID NO:1 (cross-referenced as SEQ ID NO:9), or from base 29871 to 30234 of SEQ ID NO:1 (cross-referenced as SEQ ID NO:19).

7. The method ofclaim 1, wherein the step of analyzing the DNA sample is by polymerase chain reaction (PCR).

8. The method ofclaim 7, wherein the step of PCR further comprises:

providing a forward primer which binds specifically to a first selected DNA upstream region, said first selected DNA upstream region corresponding to between bases 3000 and 6491 of SEQ ID NO:1;

providing a reverse primer which binds specifically to a second selected DNA downstream region, said selected DNA downstream region corresponding to between bases 29871 and 35035 of SEQ ID NO:1; and

performing PCR amplification such that said forward and reverse primer generate an amplified DNA product only in the presence of a DNA sample comprising the deletion mutation associated with AM.

9. The method ofclaim 8, wherein the forward primer has a sequence that is SEQ ID NO:11 and the reverse primer has a sequence that is a reverse complement to SEQ ID NO:12 (cross-referenced as SEQ ID NO:13).

10. The method ofclaim 8 further comprising providing a third primer, said third primer capable of specific binding to at least a portion of the middle region of DNA, said middle region corresponding to a DNA sequence encompassed by bases 6507 and 7500 of SEQ ID NO:1, wherein DNA that contains said middle region results in amplification of a first DNA product by said forward primer and said third primer, and wherein DNA that does not contain said middle region results in amplification of a second DNA product by said forward primer and said reverse primer.

11. The method ofclaim 10, wherein the third primer has a sequence that is a reverse complement of SEQ ID NO:14 (cross-referenced as SEQ ID NO:15).

12. The method ofclaim 10, wherein said amplified first DNA product and second DNA product have lengths that are at least 10% different, said method further comprising:

determining the length of the amplified DNA product; and

identifying the presence or absence of the AM mutation based on said determined length.

13. The method ofclaim 7 further comprising providing a forward primer and a reverse primer, wherein said forward primer is capable of specific binding to said middle region of the DNA, and said reverse primer is capable of specific binding to said middle region of the DNA, wherein said binding regions are different and the primers are capable of generating an amplification DNA product only if the DNA sample does not comprise a mutation associated with AM.

14. The method ofclaim 1 further comprising

providing a probe or primer that specifically binds to the sample of DNA having said upstream region and said downstream region in a contiguous configuration; and

identifying the sample as containing a mutation gene associated with AM for DNA samples that hybridize with said probe or primer.

15. The method ofclaim 1, wherein the analyzing the DNA sample further comprises providing a DNA probe or primer, wherein said DNA probe or primer specifically binds to said middle region.

16. The method ofclaim 1, wherein said analyzing the DNA sample comprises DNA sequencing.

17. The method ofclaim 1, wherein said analyzing the DNA sample comprises providing a probe or primer comprising a purified oligonucleotide, wherein the oligonucleotide has a length between about 15 to 50 nucleotides and specifically binds to a target sequence of SEQ ID NO:3 or complement thereof without binding to SEQ ID NO:7 or SEQ ID NO:9.

18. The method ofclaim 1, wherein said analyzing the DNA of the bovine subject comprises providing a probe or primer comprising a purified oligonucleotide, wherein the oligonucleotide has a length between about 15 to 50 nucleotides and specifically binds a breakpoint mutation region in the bovine genome, said breakpoint located between bases T429 and G430, 445A and 446C, or both of SEQ ID NO:2.

19. The method ofclaim 1, wherein the bovine is an Angus or Angus composite.

20. The method ofclaim 1, wherein the DNA sample is obtained from blood or semen.

21. A method for screening a bovine to determine if said bovine carries a mutation for AM, said method comprising:

providing a biological sample which was removed from said bovine to be screened; and

conducting a biological assay to determine the presence of a mutation in the gene responsible for AM, wherein the mutation comprises a deletion of bases 6507 to 29870 in SEQ ID NO:1 (cross-referenced as SEQ ID NO:3).

22. An oligonucleotide for diagnosing heterozygous carriers of AM, wherein the oligonucleotide has a length of 15 to 80 nucleotides, and having a region, wherein the region is identical or a reverse complement to a sequence of an at least fifteen-nucleotide segment of SEQ ID NO:1 or SEQ ID NO:2.

23. The oligonucleotide ofclaim 22, wherein said oligonucleotide is DNA.

24. The oligonucleotide ofclaim 22, wherein the region is identical to the portion of SEQ ID NO:2 comprising bases 429 and 430 or bases 445 and 446.

25. A kit for assaying for the presence of an AM marker in a bovine DNA, said kit comprising oligonucleotide sequences ofclaim 22 for PCR priming or probing for the presence or absence of a deletion mutation in the bovine genome associated with AM.

26. The kit ofclaim 25 wherein the oligonucleotide sequences comprise:

a first primer that specifically binds an upstream region, wherein said upstream region comprises at least a portion of bases 5000 to 6491 of SEQ ID NO:1, and wherein said upstream region has an ending at base number 6491 or 6507 of SEQ ID NO:1; and

a second primer that specifically binds a downstream region, wherein said downstream region comprises at least a portion of bases 29,871 to 31,000 of SEQ ID NO:1, and wherein said downstream region has a beginning corresponding to base 29,855 or 29,871 of SEQ ID NO:1,

wherein generation of an amplified DNA product by hybridization of the first primer and the second primer to said DNA indicates presence of an AM marker.

27. The kit ofclaim 26, further comprising:

a third primer that specifically binds a middle region, wherein said middle region comprises at least a portion of bases 6507 to 29,886 or 6491 to 29,870 of SEQ ID NO:1.

28. The kit ofclaim 25 further comprising a positive control and a negative control, wherein said positive control comprises a functional fragment of the DNA sequence of SEQ ID NO:2, said sequence comprising a breakpoint region located between bases 429 and 430 or between bases 445 and 446 of SEQ ID NO:2, and wherein said negative control comprises a functional fragment of the DNA sequence of SEQ ID NO:1, said fragment comprising bases 6491 to 29,871 of SEQ ID NO:1.

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